HEADER BIOSYNTHETIC PROTEIN 18-DEC-17 6BXM TITLE CRYSTAL STRUCTURE OF CANDIDATUS METHANOPEREDENS NITROREDUCENS DPH2 TITLE 2 WITH 4FE-4S CLUSTER AND SAM/CLEAVED SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHAMIDE BIOSYNTHESIS ENZYME DPH2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS METHANOPEREDENS NITROREDUCENS; SOURCE 3 ORGANISM_TAXID: 1392998; SOURCE 4 GENE: ANME2D_01646; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIPHTHAMIDE BIOSYNTHESIS, RADICAL SAM ENZYME, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.K.FENWICK,A.T.TORELLI,Y.ZHANG,M.DONG,V.KATHIRESAN,J.D.CARANTOA, AUTHOR 2 B.DZIKOVSKI,K.M.LANCASTER,J.H.FREED,B.M.HOFFMAN,H.LIN,S.E.EALICK REVDAT 3 15-NOV-23 6BXM 1 REMARK REVDAT 2 04-OCT-23 6BXM 1 LINK REVDAT 1 11-APR-18 6BXM 0 JRNL AUTH M.DONG,V.KATHIRESAN,M.K.FENWICK,A.T.TORELLI,Y.ZHANG, JRNL AUTH 2 J.D.CARANTO,B.DZIKOVSKI,A.SHARMA,K.M.LANCASTER,J.H.FREED, JRNL AUTH 3 S.E.EALICK,B.M.HOFFMAN,H.LIN JRNL TITL ORGANOMETALLIC AND RADICAL INTERMEDIATES REVEAL MECHANISM OF JRNL TITL 2 DIPHTHAMIDE BIOSYNTHESIS. JRNL REF SCIENCE V. 359 1247 2018 JRNL REFN ESSN 1095-9203 JRNL PMID 29590073 JRNL DOI 10.1126/SCIENCE.AAO6595 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 30423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.8246 - 5.0071 0.99 2782 164 0.1656 0.2047 REMARK 3 2 5.0071 - 3.9748 1.00 2685 145 0.1424 0.1940 REMARK 3 3 3.9748 - 3.4725 0.99 2620 156 0.1634 0.2042 REMARK 3 4 3.4725 - 3.1551 1.00 2641 142 0.1820 0.2472 REMARK 3 5 3.1551 - 2.9290 1.00 2616 129 0.1961 0.2631 REMARK 3 6 2.9290 - 2.7563 1.00 2642 126 0.1919 0.2340 REMARK 3 7 2.7563 - 2.6183 1.00 2593 132 0.1891 0.2374 REMARK 3 8 2.6183 - 2.5043 1.00 2593 148 0.1904 0.2504 REMARK 3 9 2.5043 - 2.4079 1.00 2586 137 0.1926 0.2917 REMARK 3 10 2.4079 - 2.3248 1.00 2604 136 0.2013 0.2795 REMARK 3 11 2.3248 - 2.2521 0.96 2534 112 0.2185 0.2799 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4962 REMARK 3 ANGLE : 0.929 6757 REMARK 3 CHIRALITY : 0.059 789 REMARK 3 PLANARITY : 0.005 859 REMARK 3 DIHEDRAL : 18.772 2997 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30482 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.57900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3LZC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65 MM HEPES, PH 6.5-7.0, AND 18-25% REMARK 280 (W/V) POLYETHYLENE GLYCOL (PEG) 1000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.94350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.18400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.18400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.94350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.04000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 SER A 1 REMARK 465 GLU A 2 REMARK 465 GLN A 3 REMARK 465 PHE A 4 REMARK 465 ASP A 5 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 GLU B 2 REMARK 465 GLN B 3 REMARK 465 PHE B 4 REMARK 465 ASP B 5 REMARK 465 GLY B 146 REMARK 465 ASP B 147 REMARK 465 ILE B 322 REMARK 465 GLN B 323 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 ASP A 17 CG OD1 OD2 REMARK 470 ARG A 33 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ASN A 113 CG OD1 ND2 REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 151 CG1 CG2 CD1 REMARK 470 ASP A 167 CG OD1 OD2 REMARK 470 ILE A 178 CG1 CG2 CD1 REMARK 470 PHE A 198 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 200 CG OD1 ND2 REMARK 470 SER A 206 OG REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 THR A 222 OG1 CG2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 ARG A 312 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 10 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 LYS B 21 CG CD CE NZ REMARK 470 GLU B 84 CG CD OE1 OE2 REMARK 470 TYR B 85 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 86 CG CD OE1 OE2 REMARK 470 ASN B 113 CG OD1 ND2 REMARK 470 ARG B 114 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 128 CG CD OE1 OE2 REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 ILE B 151 CG1 CG2 CD1 REMARK 470 LYS B 189 CG CD CE NZ REMARK 470 SER B 206 OG REMARK 470 GLU B 208 CG CD OE1 OE2 REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 225 CG CD CE NZ REMARK 470 GLU B 268 CG CD OE1 OE2 REMARK 470 LYS B 274 CG CD CE NZ REMARK 470 GLU B 292 CG CD OE1 OE2 REMARK 470 ARG B 312 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 315 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 93 84.83 53.58 REMARK 500 ASP A 263 -80.69 -96.52 REMARK 500 ALA A 282 -157.49 -92.27 REMARK 500 CYS A 283 117.52 -38.68 REMARK 500 MET B 82 158.62 178.23 REMARK 500 ASP B 263 -79.81 -94.07 REMARK 500 LYS B 274 48.15 -94.80 REMARK 500 ALA B 282 -150.42 -87.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 SF4 A 401 S2 112.2 REMARK 620 3 SF4 A 401 S3 113.7 105.9 REMARK 620 4 SF4 A 401 S4 114.1 105.5 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 159 SG REMARK 620 2 SF4 A 401 S1 116.9 REMARK 620 3 SF4 A 401 S3 115.5 105.5 REMARK 620 4 SF4 A 401 S4 114.2 99.8 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 283 SG REMARK 620 2 SF4 A 401 S1 116.6 REMARK 620 3 SF4 A 401 S2 109.9 103.0 REMARK 620 4 SF4 A 401 S4 115.8 104.7 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAM A 402 N REMARK 620 2 SF4 A 401 S1 138.8 REMARK 620 3 SF4 A 401 S2 96.7 99.5 REMARK 620 4 SF4 A 401 S3 106.1 106.0 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 61 SG REMARK 620 2 SF4 B 401 S2 110.4 REMARK 620 3 SF4 B 401 S3 116.1 105.3 REMARK 620 4 SF4 B 401 S4 114.6 106.1 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 159 SG REMARK 620 2 SF4 B 401 S1 120.4 REMARK 620 3 SF4 B 401 S3 111.6 105.1 REMARK 620 4 SF4 B 401 S4 114.1 101.5 102.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 283 SG REMARK 620 2 SF4 B 401 S1 112.0 REMARK 620 3 SF4 B 401 S2 109.6 103.1 REMARK 620 4 SF4 B 401 S4 118.9 106.0 105.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ABA B 402 N REMARK 620 2 SF4 B 401 S1 112.9 REMARK 620 3 SF4 B 401 S2 143.9 98.2 REMARK 620 4 SF4 B 401 S3 85.8 106.5 103.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ABA B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MTA B 403 DBREF1 6BXM A 2 323 UNP A0A062UZ78_9EURY DBREF2 6BXM A A0A062UZ78 2 323 DBREF1 6BXM B 2 323 UNP A0A062UZ78_9EURY DBREF2 6BXM B A0A062UZ78 2 323 SEQADV 6BXM GLY A -3 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM SER A -2 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM HIS A -1 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM MET A 0 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM SER A 1 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM GLY B -3 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM SER B -2 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM HIS B -1 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM MET B 0 UNP A0A062UZ7 EXPRESSION TAG SEQADV 6BXM SER B 1 UNP A0A062UZ7 EXPRESSION TAG SEQRES 1 A 327 GLY SER HIS MET SER GLU GLN PHE ASP PHE ASP LEU GLU SEQRES 2 A 327 ARG ILE LEU LYS THR ILE LYS ASP LYS ASN CYS LYS LYS SEQRES 3 A 327 VAL GLY LEU GLN PHE PRO GLU GLY LEU LYS ARG GLN ALA SEQRES 4 A 327 ILE ASN ILE ALA ARG GLU ILE GLU GLU LYS THR ARG ALA SEQRES 5 A 327 ASN VAL ILE ILE SER GLY ASN PRO CYS PHE GLY ALA CYS SEQRES 6 A 327 ASP ILE ASP THR ILE LEU ALA GLY SER VAL ASP ILE LEU SEQRES 7 A 327 PHE HIS PHE GLY HIS ALA GLY MET GLY GLU TYR GLU ASN SEQRES 8 A 327 VAL VAL PHE ILE GLU ALA ARG SER ASN ILE ASP ILE ILE SEQRES 9 A 327 PRO ALA VAL LYS THR ALA LEU ASN LEU LEU LYS ALA ASN SEQRES 10 A 327 ARG ILE GLY LEU ILE THR THR VAL GLN HIS VAL HIS LYS SEQRES 11 A 327 LEU GLU GLU ALA CYS LYS VAL ILE LYS GLU TYR GLY LYS SEQRES 12 A 327 GLU CYS VAL ILE GLY LYS GLY ASP PRO ARG ALA ILE TYR SEQRES 13 A 327 PRO GLY GLN VAL LEU GLY CYS ASN PHE THR ALA ALA ARG SEQRES 14 A 327 VAL ASP CYS GLU GLU PHE ILE TYR ILE GLY SER GLY ILE SEQRES 15 A 327 PHE HIS PRO LEU GLY VAL ALA ILE ALA THR LYS LYS ARG SEQRES 16 A 327 VAL ILE ALA ALA ASP PRO PHE LEU ASN GLN ALA VAL GLU SEQRES 17 A 327 VAL SER PRO GLU ARG PHE LEU ARG LYS ARG GLY GLY TYR SEQRES 18 A 327 ILE ALA LYS ALA THR GLY ALA LYS ILE PHE GLY ILE ILE SEQRES 19 A 327 VAL SER THR LYS SER GLY GLN TYR ARG MET LYS LEU ALA SEQRES 20 A 327 GLN LYS LEU LYS GLU ILE ALA ASP LYS HIS GLY LYS ILE SEQRES 21 A 327 GLY TYR ILE ILE LEU MET ASP LEU VAL THR PRO GLU GLN SEQRES 22 A 327 LEU LEU ALA PHE LYS ALA ASP ALA TYR VAL ASN THR ALA SEQRES 23 A 327 CYS PRO ARG ILE THR ILE ASP ASP ALA GLU ARG PHE HIS SEQRES 24 A 327 ALA PRO VAL LEU THR PRO GLN GLU PHE GLU ILE VAL LEU SEQRES 25 A 327 GLY GLU ARG ARG TRP GLU ASN MET GLU MET ASP GLU MET SEQRES 26 A 327 ILE GLN SEQRES 1 B 327 GLY SER HIS MET SER GLU GLN PHE ASP PHE ASP LEU GLU SEQRES 2 B 327 ARG ILE LEU LYS THR ILE LYS ASP LYS ASN CYS LYS LYS SEQRES 3 B 327 VAL GLY LEU GLN PHE PRO GLU GLY LEU LYS ARG GLN ALA SEQRES 4 B 327 ILE ASN ILE ALA ARG GLU ILE GLU GLU LYS THR ARG ALA SEQRES 5 B 327 ASN VAL ILE ILE SER GLY ASN PRO CYS PHE GLY ALA CYS SEQRES 6 B 327 ASP ILE ASP THR ILE LEU ALA GLY SER VAL ASP ILE LEU SEQRES 7 B 327 PHE HIS PHE GLY HIS ALA GLY MET GLY GLU TYR GLU ASN SEQRES 8 B 327 VAL VAL PHE ILE GLU ALA ARG SER ASN ILE ASP ILE ILE SEQRES 9 B 327 PRO ALA VAL LYS THR ALA LEU ASN LEU LEU LYS ALA ASN SEQRES 10 B 327 ARG ILE GLY LEU ILE THR THR VAL GLN HIS VAL HIS LYS SEQRES 11 B 327 LEU GLU GLU ALA CYS LYS VAL ILE LYS GLU TYR GLY LYS SEQRES 12 B 327 GLU CYS VAL ILE GLY LYS GLY ASP PRO ARG ALA ILE TYR SEQRES 13 B 327 PRO GLY GLN VAL LEU GLY CYS ASN PHE THR ALA ALA ARG SEQRES 14 B 327 VAL ASP CYS GLU GLU PHE ILE TYR ILE GLY SER GLY ILE SEQRES 15 B 327 PHE HIS PRO LEU GLY VAL ALA ILE ALA THR LYS LYS ARG SEQRES 16 B 327 VAL ILE ALA ALA ASP PRO PHE LEU ASN GLN ALA VAL GLU SEQRES 17 B 327 VAL SER PRO GLU ARG PHE LEU ARG LYS ARG GLY GLY TYR SEQRES 18 B 327 ILE ALA LYS ALA THR GLY ALA LYS ILE PHE GLY ILE ILE SEQRES 19 B 327 VAL SER THR LYS SER GLY GLN TYR ARG MET LYS LEU ALA SEQRES 20 B 327 GLN LYS LEU LYS GLU ILE ALA ASP LYS HIS GLY LYS ILE SEQRES 21 B 327 GLY TYR ILE ILE LEU MET ASP LEU VAL THR PRO GLU GLN SEQRES 22 B 327 LEU LEU ALA PHE LYS ALA ASP ALA TYR VAL ASN THR ALA SEQRES 23 B 327 CYS PRO ARG ILE THR ILE ASP ASP ALA GLU ARG PHE HIS SEQRES 24 B 327 ALA PRO VAL LEU THR PRO GLN GLU PHE GLU ILE VAL LEU SEQRES 25 B 327 GLY GLU ARG ARG TRP GLU ASN MET GLU MET ASP GLU MET SEQRES 26 B 327 ILE GLN HET SF4 A 401 8 HET SAM A 402 27 HET SF4 B 401 8 HET ABA B 402 7 HET MTA B 403 20 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SAM S-ADENOSYLMETHIONINE HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE FORMUL 3 SF4 2(FE4 S4) FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 6 ABA C4 H9 N O2 FORMUL 7 MTA C11 H15 N5 O3 S FORMUL 8 HOH *200(H2 O) HELIX 1 AA1 ASP A 7 ASN A 19 1 13 HELIX 2 AA2 PRO A 28 ARG A 33 5 6 HELIX 3 AA3 GLN A 34 THR A 46 1 13 HELIX 4 AA4 ASP A 64 GLY A 69 1 6 HELIX 5 AA5 ILE A 99 ASN A 108 1 10 HELIX 6 AA6 HIS A 123 HIS A 125 5 3 HELIX 7 AA7 LYS A 126 TYR A 137 1 12 HELIX 8 AA8 PHE A 161 ARG A 165 5 5 HELIX 9 AA9 ILE A 178 LYS A 189 1 12 HELIX 10 AB1 PRO A 207 ALA A 221 1 15 HELIX 11 AB2 ARG A 239 HIS A 253 1 15 HELIX 12 AB3 THR A 266 ALA A 272 1 7 HELIX 13 AB4 CYS A 283 ASP A 290 1 8 HELIX 14 AB5 ALA A 291 PHE A 294 5 4 HELIX 15 AB6 THR A 300 GLY A 309 1 10 HELIX 16 AB7 ARG A 312 MET A 316 5 5 HELIX 17 AB8 ASP B 7 LYS B 18 1 12 HELIX 18 AB9 LEU B 31 ARG B 33 5 3 HELIX 19 AC1 GLN B 34 THR B 46 1 13 HELIX 20 AC2 ASP B 64 SER B 70 1 7 HELIX 21 AC3 ILE B 99 ASN B 108 1 10 HELIX 22 AC4 VAL B 121 HIS B 125 5 5 HELIX 23 AC5 LYS B 126 TYR B 137 1 12 HELIX 24 AC6 PHE B 161 ARG B 165 5 5 HELIX 25 AC7 ILE B 178 LYS B 189 1 12 HELIX 26 AC8 PRO B 207 GLY B 223 1 17 HELIX 27 AC9 ARG B 239 HIS B 253 1 15 HELIX 28 AD1 THR B 266 ALA B 272 1 7 HELIX 29 AD2 CYS B 283 ASP B 290 1 8 HELIX 30 AD3 ALA B 291 PHE B 294 5 4 HELIX 31 AD4 THR B 300 LEU B 308 1 9 HELIX 32 AD5 ARG B 312 MET B 316 5 5 SHEET 1 AA1 8 VAL A 88 ILE A 91 0 SHEET 2 AA1 8 ILE A 73 PHE A 77 1 N LEU A 74 O VAL A 89 SHEET 3 AA1 8 LYS A 22 GLN A 26 1 N GLY A 24 O PHE A 75 SHEET 4 AA1 8 ASN A 49 SER A 53 1 O ILE A 51 N VAL A 23 SHEET 5 AA1 8 ILE B 256 MET B 262 1 O ILE B 259 N ILE A 52 SHEET 6 AA1 8 ILE B 226 SER B 232 1 N ILE B 229 O TYR B 258 SHEET 7 AA1 8 ALA B 277 ASN B 280 1 O VAL B 279 N ILE B 230 SHEET 8 AA1 8 VAL B 298 LEU B 299 1 O LEU B 299 N TYR B 278 SHEET 1 AA2 5 GLU A 140 VAL A 142 0 SHEET 2 AA2 5 ARG A 114 THR A 119 1 N ILE A 115 O GLU A 140 SHEET 3 AA2 5 GLU A 170 ILE A 174 1 O GLU A 170 N GLY A 116 SHEET 4 AA2 5 ARG A 191 ASP A 196 1 O ALA A 195 N TYR A 173 SHEET 5 AA2 5 GLN A 201 VAL A 205 -1 O VAL A 203 N ALA A 194 SHEET 1 AA3 8 VAL A 298 LEU A 299 0 SHEET 2 AA3 8 ALA A 277 ASN A 280 1 N TYR A 278 O LEU A 299 SHEET 3 AA3 8 ILE A 226 SER A 232 1 N GLY A 228 O VAL A 279 SHEET 4 AA3 8 ILE A 256 MET A 262 1 O ILE A 256 N PHE A 227 SHEET 5 AA3 8 ASN B 49 SER B 53 1 O ILE B 52 N LEU A 261 SHEET 6 AA3 8 LYS B 22 GLN B 26 1 N LEU B 25 O SER B 53 SHEET 7 AA3 8 ILE B 73 PHE B 77 1 O PHE B 75 N GLY B 24 SHEET 8 AA3 8 VAL B 88 ILE B 91 1 O ILE B 91 N HIS B 76 SHEET 1 AA4 5 GLU B 140 ILE B 143 0 SHEET 2 AA4 5 ARG B 114 THR B 119 1 N ILE B 115 O GLU B 140 SHEET 3 AA4 5 GLU B 170 ILE B 174 1 O GLU B 170 N GLY B 116 SHEET 4 AA4 5 ARG B 191 ASP B 196 1 O ALA B 195 N TYR B 173 SHEET 5 AA4 5 GLN B 201 VAL B 205 -1 O VAL B 203 N ALA B 194 LINK SG CYS A 61 FE1 SF4 A 401 1555 1555 2.30 LINK SG CYS A 159 FE2 SF4 A 401 1555 1555 2.21 LINK SG CYS A 283 FE3 SF4 A 401 1555 1555 2.25 LINK FE4 SF4 A 401 N SAM A 402 1555 1555 2.26 LINK SG CYS B 61 FE1 SF4 B 401 1555 1555 2.25 LINK SG CYS B 159 FE2 SF4 B 401 1555 1555 2.27 LINK SG CYS B 283 FE3 SF4 B 401 1555 1555 2.28 LINK FE4 SF4 B 401 N ABA B 402 1555 1555 2.66 SITE 1 AC1 6 CYS A 61 GLY A 158 CYS A 159 CYS A 283 SITE 2 AC1 6 ARG A 285 SAM A 402 SITE 1 AC2 17 PHE A 58 LEU A 157 GLY A 158 HIS A 180 SITE 2 AC2 17 LYS A 234 GLN A 237 ASP A 263 LEU A 264 SITE 3 AC2 17 VAL A 265 CYS A 283 ARG A 285 ILE A 286 SITE 4 AC2 17 ASP A 289 ASP A 290 SF4 A 401 HOH A 558 SITE 5 AC2 17 HOH A 561 SITE 1 AC3 6 CYS B 61 GLY B 158 CYS B 159 CYS B 283 SITE 2 AC3 6 ARG B 285 ABA B 402 SITE 1 AC4 7 PHE B 58 LEU B 157 GLY B 158 HIS B 180 SITE 2 AC4 7 ARG B 285 SF4 B 401 MTA B 403 SITE 1 AC5 13 PHE B 58 SER B 232 LYS B 234 GLN B 237 SITE 2 AC5 13 ASP B 263 LEU B 264 VAL B 265 CYS B 283 SITE 3 AC5 13 ILE B 286 ASP B 289 ASP B 290 ABA B 402 SITE 4 AC5 13 HOH B 539 CRYST1 61.887 64.080 158.368 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016158 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006314 0.00000